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12

tldr; it depends on flexibility / number of rotatable bonds A while ago, I answered a related question - in general, molecules with fewer "rotatable bonds" need fewer conformers geometries generated to sample properly. Based on that, I would normally have said "50 is more than enough for up to 3-4 rotatable bonds" and beyond that, I'd ...


8

LocVib (part of MoViPac) I have never used VEDA before, but according to the paper, it decomposes the normal modes into vibrations of atomic groups, bond stretching, bending or something else. Something similar is LocVib, which localizes normal modes to localized vibrational modes by maximizing the "distances" between vibrational modes and "...


8

I assume you're referring to eq 51 of the Hirata-Head-Gordon-Bartlett paper. One should note that these are not two-electron integrals, since there is only one spatial position; these are rather weighted four-center one-electron integrals. As always, the problem when you have four indices is that there is a huge number of integrals that come out, and you ...


5

"I was able to guess most of results, except the ones with value 0.663472." I am able to confirm that your integrals are correct even for the 0.663472 case, because by calculating them myself in MOLPRO (a completely different program from what you used), I get the same indices of 2 2 1 1: &FCI NORB= 2,NELEC= 2,MS2= 0, ORBSYM=1,5,ISYM=0, 0....


5

PySCF and Psi4 both implement analytical geometric Hessians for Hartree-Fock calculations. The computation of the geometric Hessian indeed requires solving the coupled perturbed Hartree-Fock equations: while one can evaluate the force acting on the nuclei just with the SCF wave function and the integral derivatives, the second derivative also contains a ...


5

The derivatives of a molecular Hamiltonian with respect to nuclear coordinates can be performed analytically (as you correctly pointed out), and therefore does not need PySCF or Psi4, which are programs for doing numerical calculations for things that cannot be done analytically. This is how it's done: \begin{align} H &= -\sum_{i}\frac{1}{2}\nabla_{i}^{2}...


5

As you already figured out, the error is that the charge and multiplicity are inconsistent with the molecule; this is what Psi4 tells you: qcelemental.exceptions.ValidationError: Inconsistent or unspecified chg/mult: sys chg: None, frag chg: [0.0], sys mult: None, frag mult: [1] The problem is that the system has 111 electrons, which is an odd number, so ...


5

At a rough guess you can assume that the number of conformers you need to generate (N_conf) is directly proportional to the number of rotatable bonds (N_rot) in a given compound. I seem to recall that this number (of rotatable bonds) is something you can easily calculate, e.g., with openbabel. So the number of conformers you request for a given compound ...


4

I would like to post a partial answer that I have for now. For the indices ijkl in the FCIDUMP file, it corresponds to the integral (see https://theochem.github.io/horton/2.0.2/user_hamiltonian_io.html) $$ \tag{1} \int dx_1dx_2\chi_i^*(x_1)\chi_k^*(x_2)\chi_j(x_1)\chi_l(x_2) $$ while the indices in the paper, it is $$ \tag{2} \int dx_1dx_2\chi_i^*(x_1)\chi_j^...


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